Hi, Jianhong:

Thank you very much and I just checked the file you sent to me,  and  returned to the ChIPPeakAnno program followed Julie's code,  I found the output only part of the row,
the showed data is 7142, and after this number, all of the peak was  deleted from output dataset:

7141            425497             NearestStart
7142            426447             NearestStart
[ reached getOption("max.print") -- omitted 34386 rows ]]


output 7142 +omitted 34386= 41528 rows you showed to me,  I don't know why only got partial data output?
if I can get the results for my exon, intron or other regions peaks? I just followed Julie's code as following:

to show the peaks from exons:

>annotatedPeak = annotatePeakInBatch(ma, AnnotationData=Exon.human.NCBI36)

or to show the peaks from intron as following:

>annotatedPeak = annotatePeakInBatch(ma, AnnotationData=Intron.human.NCBI36)

is right?

Thanks again for your nice help!

Xianyong




On Mar 19, 2012, at 11:10 AM, Ou, Jianhong wrote:

Hi Xian-Yong,

I opened you bed file and found that there are 41528 rows in the file. If you only annotate the first 5000 rows, you should get the annotation for the first 5000 rows. So please try Julie's code again. I also copied my output here and hope this will help you.

> setwd("/Users/jianhongou/Documents/Julie")
> library(ChIPpeakAnno)
Loading required package: biomaRt
Loading required package: multtest
Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

Loading required package: IRanges

Attaching package: ‘IRanges’

The following object(s) are masked from ‘package:Biobase’:

    updateObject

The following object(s) are masked from ‘package:base’:

    cbind, eval, intersect, Map, mapply, order, paste, pmax, pmax.int, pmin, pmin.int, rbind, rep.int, setdiff, table, union

Loading required package: Biostrings
Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: BSgenome.Ecoli.NCBI.20080805
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: DBI

Loading required package: org.Hs.eg.db

Loading required package: limma
Loading required package: gplots
Loading required package: gtools
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

Attaching package: ‘gdata’

The following object(s) are masked from ‘package:IRanges’:

    trim

The following object(s) are masked from ‘package:Biobase’:

    combine

The following object(s) are masked from ‘package:stats’:

    nobs

The following object(s) are masked from ‘package:utils’:

    object.size

Loading required package: caTools
Loading required package: bitops

Attaching package: ‘caTools’

The following object(s) are masked from ‘package:IRanges’:

    runmean

Loading required package: grid
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

Attaching package: ‘gplots’

The following object(s) are masked from ‘package:IRanges’:

    space

The following object(s) are masked from ‘package:multtest’:

    wapply

The following object(s) are masked from ‘package:stats’:

    lowess

Warning messages:
1: package ‘AnnotationDbi’ was built under R version 2.14.2
2: package ‘limma’ was built under R version 2.14.2
3: replacing previous import ‘space’ when loading ‘IRanges’
> ?annotatePeakInBatch
starting httpd help server ... done
> data(TSS.human.NCBI36)
> ma<-read.delim("ma2.bed",header=F)
> head(ma)
    V1     V2     V3
1 chr1   9949  10500
2 chr1 114849 115000
3 chr1 115749 115850
4 chr1 117649 117750
5 chr1 123749 123850
6 chr1 124249 124400
> colnames(ma)<-c("chrom","chromStart","chromEnd")
> ma.rd<-BED2RangedData(ma)
> head(ma.rd)
RangedData with 6 rows and 2 value columns across 25 spaces
         space           ranges |    strand     score
      <factor>        <IRanges> | <numeric> <numeric>
00001        1 [  9949,  10500] |         1         1
00002        1 [114849, 115000] |         1         1
00003        1 [115749, 115850] |         1         1
00004        1 [117649, 117750] |         1         1
00005        1 [123749, 123850] |         1         1
00006        1 [124249, 124400] |         1         1
> tail(ma.rd)
RangedData with 6 rows and 2 value columns across 25 spaces
         space               ranges |    strand     score
      <factor>            <IRanges> | <numeric> <numeric>
41523        Y [58996299, 58997400] |         1         1
41524        Y [58997549, 58997800] |         1         1
41525        Y [59005049, 59005250] |         1         1
41526        Y [59020749, 59020850] |         1         1
41527        Y [59024149, 59024300] |         1         1
41528        Y [59027749, 59027900] |         1         1
> tail(ma)
      chrom chromStart chromEnd
41523  chrY   58996299 58997400
41524  chrY   58997549 58997800
41525  chrY   59005049 59005250
41526  chrY   59020749 59020850
41527  chrY   59024149 59024300
41528  chrY   59027749 59027900
> annotatedPeak<-annotatePeakInBatch(ma.rd[1:5000,],AnnotationData=TSS.human.NCBI36)
> tail(annotatedPeak)
RangedData with 6 rows and 9 value columns across 2 spaces
                         space               ranges |        peak      strand         feature start_position end_position insideFeature distancetoFeature shortestDistance
                      <factor>            <IRanges> | <character> <character>     <character>      <numeric>    <numeric>   <character>         <numeric>        <numeric>
04982 ENSG00000165606       10 [50319257, 50319808] |       04982           - ENSG00000165606       50242243     50273992      upstream            -45265            45265
04983 ENSG00000165606       10 [50328407, 50328608] |       04983           - ENSG00000165606       50242243     50273992      upstream            -54415            54415
04984 ENSG00000032514       10 [50373707, 50373808] |       04984           - ENSG00000032514       50336715     50417078        inside             43371            36992
04987 ENSG00000209936       10 [50593507, 50593808] |       04987           - ENSG00000209936       50581041     50581425      upstream            -12082            12082
04999 ENSG00000219927       10 [51192307, 51192408] |       04999           - ENSG00000219927       51202108     51202578    downstream             10271             9700
05000 ENSG00000197612       10 [51389007, 51389258] |       05000           - ENSG00000197612       51398379     51398687    downstream              9680             9121
                      fromOverlappingOrNearest
                                   <character>
04982 ENSG00000165606             NearestStart
04983 ENSG00000165606             NearestStart
04984 ENSG00000032514             NearestStart
04987 ENSG00000209936             NearestStart
04999 ENSG00000219927             NearestStart
05000 ENSG00000197612             NearestStart
> ma.rd[5000,]
RangedData with 1 row and 2 value columns across 25 spaces
         space               ranges |    strand     score
      <factor>            <IRanges> | <numeric> <numeric>
05000       10 [51389007, 51389258] |         1         1
> ma.rd[20000,]
RangedData with 1 row and 2 value columns across 25 spaces
         space               ranges |    strand     score
      <factor>            <IRanges> | <numeric> <numeric>
20000       18 [72846414, 72846715] |         1         1
> annotatedPeak<-annotatePeakInBatch(ma.rd[20000:22000,],AnnotationData=TSS.human.NCBI36)
> tail(annotatedPeak)
RangedData with 6 rows and 9 value columns across 3 spaces
                         space               ranges |        peak      strand         feature start_position end_position insideFeature distancetoFeature shortestDistance
                      <factor>            <IRanges> | <character> <character>     <character>      <numeric>    <numeric>   <character>         <numeric>        <numeric>
21971 ENSG00000207350        2 [88480587, 88481138] |       21971           - ENSG00000207350       88495532     88495638    downstream             15051            14394
21973 ENSG00000172071        2 [88679537, 88679688] |       21973           - ENSG00000172071       88637376     88708209        inside             28672            28521
21974 ENSG00000172071        2 [88739987, 88740138] |       21974           - ENSG00000172071       88637376     88708209      upstream            -31778            31778
21975 ENSG00000211592        2 [88906287, 88906388] |       21975           - ENSG00000211592       88937989     88938311    downstream             32024            31601
21977 ENSG00000220770        2 [89219237, 89219338] |       21977           - ENSG00000220770       89215573     89215855      upstream             -3382             3382
21978 ENSG00000211619        2 [89462437, 89462638] |       21978           - ENSG00000211619       89410986     89411308      upstream            -51129            51129
                      fromOverlappingOrNearest
                                   <character>
21971 ENSG00000207350             NearestStart
21973 ENSG00000172071             NearestStart
21974 ENSG00000172071             NearestStart
21975 ENSG00000211592             NearestStart
21977 ENSG00000220770             NearestStart
21978 ENSG00000211619             NearestStart
> ma.rd[21971:21978,]
RangedData with 8 rows and 2 value columns across 25 spaces
         space               ranges |    strand     score
      <factor>            <IRanges> | <numeric> <numeric>
21971        2 [88480587, 88481138] |         1         1
21972        2 [88603637, 88603888] |         1         1
21973        2 [88679537, 88679688] |         1         1
21974        2 [88739987, 88740138] |         1         1
21975        2 [88906287, 88906388] |         1         1
21976        2 [88959637, 88959738] |         1         1
21977        2 [89219237, 89219338] |         1         1
21978        2 [89462437, 89462638] |         1         1
> annotatedPeak<-annotatePeakInBatch(ma.rd,AnnotationData=TSS.human.NCBI36)
> tail(annotatedPeak)
RangedData with 6 rows and 9 value columns across 25 spaces
                         space               ranges |        peak      strand         feature start_position end_position insideFeature distancetoFeature shortestDistance
                      <factor>            <IRanges> | <character> <character>     <character>      <numeric>    <numeric>   <character>         <numeric>        <numeric>
41488 ENSG00000219871        Y [28812949, 28813100] |       41488           - ENSG00000219871       27150386     27190187      upstream          -1622762          1622762
41489 ENSG00000219871        Y [28813749, 28814400] |       41489           - ENSG00000219871       27150386     27190187      upstream          -1623562          1623562
41490 ENSG00000219871        Y [28815249, 28815500] |       41490           - ENSG00000219871       27150386     27190187      upstream          -1625062          1625062
41491 ENSG00000219871        Y [28816399, 28816900] |       41491           - ENSG00000219871       27150386     27190187      upstream          -1626212          1626212
41492 ENSG00000219871        Y [28817599, 28818450] |       41492           - ENSG00000219871       27150386     27190187      upstream          -1627412          1627412
41493 ENSG00000219871        Y [28818799, 28819050] |       41493           - ENSG00000219871       27150386     27190187      upstream          -1628612          1628612
                      fromOverlappingOrNearest
                                   <character>
41488 ENSG00000219871             NearestStart
41489 ENSG00000219871             NearestStart
41490 ENSG00000219871             NearestStart
41491 ENSG00000219871             NearestStart
41492 ENSG00000219871             NearestStart
41493 ENSG00000219871             NearestStart
> write.csv(as.data.frame(annotatedPeak),"ma.annotatedPeak.031912.csv",row.names=F)
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] ChIPpeakAnno_2.2.0                  gplots_2.10.1                       KernSmooth_2.23-7                   caTools_1.12
 [5] bitops_1.0-4.1                      gdata_2.8.2                         gtools_2.6.2                        limma_3.10.3
 [9] org.Hs.eg.db_2.6.4                  GO.db_2.6.1                         RSQLite_0.11.1                      DBI_0.2-5
[13] AnnotationDbi_1.16.19               BSgenome.Ecoli.NCBI.20080805_1.3.17 BSgenome_1.22.0                     GenomicRanges_1.6.7
[17] Biostrings_2.22.0                   IRanges_1.12.6                      multtest_2.10.0                     Biobase_2.14.0
[21] biomaRt_2.10.0

loaded via a namespace (and not attached):
[1] MASS_7.3-17      RCurl_1.91-1     splines_2.14.1   survival_2.36-12 tools_2.14.1     XML_3.9-4
>


Yours sincerely,

Jianhong Ou

jianhong.ou@umassmed.edu<mailto:jianhong.ou@umassmed.edu>


On Mar 19, 2012, at 10:44 AM, Zhu, Lihua (Julie) wrote:

Dear Xian-Yong,

Jianhong will help you to resolve the issues. Could you please send us the sessionInfo() output? Thanks!

Best regards,

Julie


On 3/19/12 10:05 AM, "Ma, Xian-Yong" <xian-yong.ma@yale.edu<x-msg://61/>> wrote:

Dear Julie:

When I tried your code to analyze my CHIP data, I was still got the peaks only from chromosome 1, 10 and 11, and I checked
back to the data and I found peaks distribute on all chromosomes, another question is when I tried to search the exons or introns use this program,
I can't get the results, here I attach one of my  "bed" format file of my CHIP data, would you please help me to figure out what's wrong when
I use your software? since I am struggle with this issue for several days and I am really need to use the correct code to analyze these data.

annotatedPeak = annotatePeakInBatch(ma, AnnotationData=TSS.human.NCBI36)  for TSS peak analysis?
annotatedPeak = annotatePeakInBatch(ma, AnnotationData=exon.human.NCBI36) for exon peak analysis?




I appreciate your nice help,

Best regards,


Xianyong





On Mar 16, 2012, at 1:47 PM, Zhu, Lihua (Julie) wrote:

Xianyong,

Thanks for letting me know! Good luck!

Best regards,

Julie


On 3/16/12 1:27 PM, "Ma, Xian-Yong" <xian-yong.ma@yale.edu<x-msg://61/>> wrote:

Dear Julie:

I just followed your suggestion and I got similar results, I will check my
dataset and use your code again,
hope problem is from my dataset.

Best regards,

Xianyong


On Mar 16, 2012, at 11:33 AM, Zhu, Lihua (Julie) wrote:

Dear Xianyong,

You would need to use the following code without specifying the index range
for your peak. Ma[1:6,] means the first 6 peaks.

annotatedPeak = annotatePeakInBatch(ma, AnnotationData=TSS.human.NCBI36)

Hope this resolves your issue.

Best regards,

Julie


On 3/16/12 10:24 AM, "Ma, Xian-Yong" <xian-yong.ma@yale.edu<x-msg://61/>> wrote:

Hi, Dear Dr.Zhu:

I am Xianyong Ma from Yale Medical School, I am working on a CHIP-Sequecning
project, and I try to use
ChIPPeakAnno to analysis my data, it is a wonderful tool to map the binding
sites for my purpose, now I have
trouble when I use it, I don't understand the meaning of following sentence:
annotatedPeak = annotatePeakInBatch(ma[1:6,],
AnnotationData=TSS.human.NCBI36),
when I change the [1:6] to the number [1:5000], I only got the peaks from
chromosome 1,10 and 11, I think I should get the bindings from all
chromosomes
since I check them by another method.

Thanks very much for your nice help!


sincerely,

Xianyong Ma









<ma.annotatedPeak.031912.csv.zip>


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